I thought about this for just abit but how about these sugestions:
1) Make the research tree more indepth. Maybe more points in certain talents that go past 2 points but not required to go up the tree. More researchable items in general. More then 1 super weapon available per race (but make only 1 super weapon type allowable per game).
1b) With added points and more research points to be able to be spent lower research time on earlier points by a factor of how many research stations you have. So like level 1 research points would be reduced by 25% on time with the aquisition of 4 research stations of that category.
2) More unit types. Mine layers, EMP ships, etc...and more diversity between the races. Balanced accordingly however.
2b) Titan Ships. Accessible on the 5 or 6 capital ship point. Only a 1-2 titans limit per race. Cost nearly double of what a Cap ship is.
3) Cooldown timer on long phase jumps that are between stars.
4) Make a defensive advantage for fleets in their sector, possibly influenced by culture. Example: A fleet is 1 jump away from their home planet, thusly will fighter harder and do more damage then if it was a neutral or outer sight.
5) Include other bodies of mass in gravity wells besides asteroids (moons basically

) . Allow moons to have some resource or strategic ability.
One could hope can't they.